pubmed.ncbi.nlm.nih.gov

How does a drug molecule find its target binding site? - PubMed

  • ️Sat Jan 01 2011

. 2011 Jun 22;133(24):9181-3.

doi: 10.1021/ja202726y. Epub 2011 May 13.

Affiliations

How does a drug molecule find its target binding site?

Yibing Shan et al. J Am Chem Soc. 2011.

Erratum in

  • J Am Chem Soc. 2014 Feb 26;136(8):3320

Abstract

Although the thermodynamic principles that control the binding of drug molecules to their protein targets are well understood, detailed experimental characterization of the process by which such binding occurs has proven challenging. We conducted relatively long, unguided molecular dynamics simulations in which a ligand (the cancer drug dasatinib or the kinase inhibitor PP1) was initially placed at a random location within a box that also contained a protein (Src kinase) to which that ligand was known to bind. In several of these simulations, the ligand correctly identified its target binding site, forming a complex virtually identical to the crystallographically determined bound structure. The simulated trajectories provide a continuous, atomic-level view of the entire binding process, revealing persistent and noteworthy intermediate conformations and shedding light on the role of water molecules. The technique we employed, which does not assume any prior knowledge of the binding site's location, may prove particularly useful in the development of allosteric inhibitors that target previously undiscovered binding sites.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Simulation of the binding of PP1 and dasatinib to Src kinase

(A) At top, traces of a PP1 molecule in one simulation, in which the native pose is reached in 15 µs; for clarity, only the average conformation of the protein is shown. At bottom, a density map (depicted by red iso-contour surfaces) representing the frequency of PP1 interaction on the protein surface, which is constructed based on all seven similar simulations we carried out. The high-density “hot spots” largely correspond to known ligand-binding sites (labeled) of protein kinases, but the “G-loop site” has not been identified previously. The locations of the native binding poses (N) and non-native poses (a–f) are also labeled. Multiple ligand poses may contribute to a density-map hot spot. (B) The binding poses of PP1 (from three simulations) and dasatinib (from one simulation) are superimposed onto the X-ray structures (1QCF and 3G5D, respectively). (C) The binding poses of PP1 and dasatinib adopted in simulations, which are highly consistent with the crystallographic binding poses (within 2.0 Å RMSD), represent the most favorable ligand–protein interaction energies (estimated using a generalized Born model [3]). In principle, in the absence of the X-ray structures, the native binding poses may be identified by limited conformational fluctuation and low interaction energy of the bound ligands. When PP1 is in the native pose, for instance, its conformation fluctuates up to approximately 2 Å RMSD with respect to the crystallographic binding pose (by contrast, when PP1 is in the G-loop pocket, its conformation fluctuates as much as 5 Å RMSD from an average conformation); the average interaction energy of PP1 in the native pose was found to be lower than that of PP1 in the G-loop pocket in our simulation by approximately 2 kcal/mol. As shown in (A), the non-native poses b, c, and d correspond to PP1 interacting with the P loop, the αC helix region, and the αG helix, respectively; pose a features a single layer of water molecules between the protein and the ligand (see Figure 2).

Figure 2
Figure 2. Water molecules in the simulated ligand binding and a putative allosteric binding site

(A) Ligand RMSD with respect to the native pose as a function of time, for each binding simulation; each conformation is superimposed on the X-ray structures of the protein. Poses a–f refer to non-native PP1 poses, while N refers to the native poses of PP1 and dasatinib. Specifically, b–e refer to poses in which PP1 remains for 1 µs or more, while a and f refer to poses immediately preceding the native pose. In Simulation 2, PP1 binds via an alternative pathway that circumvents pose a. Poses e and f are observed only in Simulation 2, one in the ATP-binding site and the other in the extended ATP-binding site adjacent to the αC helix. (B) Water density (blue surfaces) in the native pose and in intermediate pose a, from a PP1 binding simulation. The simulated water density for the native pose, particularly that of the enclosed water (indicated by the red arrow), mirrors that of the X-ray structure. In pose a, which immediately precedes binding, a single layer of water molecules separates the ligand from the binding pocket surface. (C) A close-up of the G-loop site occupied by PP1, which is underformed and too small to accommodate PP1 in the X-ray structure from which the simulation was initiated (PDB entry 1Y57). (D) In an intermediate state preceding dasatinib binding by 130 ns, a layer of water molecules separates dasatinib from the protein. In both (B) and (C), the protein is clipped to show the otherwise enclosed region.

Similar articles

Cited by

References

    1. Sicheri F, Moarefi I, Kuriyan J. Nature. 1997;385:602. - PubMed
    1. Getlik M, Grütter C, Simard JR, Klüter S, Rabiller M, Rode HB, Robubi A, Rauh D. J. Med. Chem. 2009;52:3915. - PubMed
    1. Onufriev A, Bashford D, Case DA. J. Phys. Chem. B. 2000;104:3712.
    1. Shan Y, Seeliger MA, Eastwood MP, Frank F, Xu H, Jensen MØ, Dror RO, Kuriyan J, Shaw DE. Proc. Natl. Acad. Sci. U.S.A. 2009;106:139. - PMC - PubMed
    1. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Proteins: Struct. Funct. Bioinf. 1995;21:167. - PubMed

MeSH terms

Substances